Clustering

This notebook will begin looking at clustering methods on the expression of the genes in a single sample of the dataset of interest, from an unbiased approach.

Set Up

# Load libraries
library(magrittr)
library(scater)
library(readr)
library(bluster)
library(ggpubr)
library(pheatmap)

# Set file paths
data_dir <- file.path("results", "Gawad_processed_data")

# Source custom functions script
source(file.path("utils", "clustering-functions.R"))

Read in data

sample_290_normalized <- read_rds(
  file.path(data_dir, "SCPCS000216", "SCPCL000290_miQC_downstream_processed_normalized_reduced_sce.rds"))

Perform clustering

k-means

# Perform k-means clustering
kmeans_cluster_names <- paste("kmeans", c(4:10), sep = "_")

sample_290_normalized <- kmeans_clustering(
  sample_290_normalized,
  k_range = c(4:10),
  check_stability = TRUE
)

# Plot k-means
kmeans_plot_list <- kmeans_cluster_names %>%
  purrr::map(~ plotReducedDim(sample_290_normalized, dimred = "UMAP", colour_by = .x) + theme_bw())

cowplot::plot_grid(plotlist = kmeans_plot_list, ncol = 4)

graph-based, walktrap

# Perform graph-based walktrap clustering
walktrap_cluster_names <- paste("walktrap", c(5, 10, 15, 20, 25), sep = "_")

sample_290_normalized <- graph_clustering(
  sample_290_normalized,
  nn_range = c(5, 10, 15, 20, 25),
  weighting_type = "rank",
  cluster_function = "walktrap",
  check_stability = TRUE
)

Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'

# Plot
walktrap_plot_list <- walktrap_cluster_names %>%
   purrr::map(~ plotReducedDim(sample_290_normalized, dimred = "UMAP", colour_by = .x) + theme_bw())

cowplot::plot_grid(plotlist = walktrap_plot_list, ncol = 3)

graph-based, louvain

# Perform graph-based louvain clustering
louvain_cluster_names <- paste("louvain", c(5, 10, 15, 20, 25), sep = "_")

sample_290_normalized <- graph_clustering(
  sample_290_normalized,
  nn_range = c(5, 10, 15, 20, 25),
  weighting_type = "jaccard",
  cluster_function = "louvain",
  check_stability = TRUE
)

Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'
Warning in (function (to_check, X, clust_centers, clust_info, dtype, nn,  :
  detected tied distances to neighbors, see ?'BiocNeighbors-ties'

# Plot
louvain_plot_list <- louvain_cluster_names %>%
   purrr::map(~ plotReducedDim(sample_290_normalized, dimred = "UMAP", colour_by = .x) + theme_bw())


cowplot::plot_grid(plotlist = louvain_plot_list, ncol = 3)

Check cluster validity stats

k-means

# Check the k-means cluster validity stats for each of the clusters and return
# stats in a data frame
kmeans_stats_df <- create_metadata_stats_df(sample_290_normalized, c(4:10), 1, "kmeans")

Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"

# Preview the results
head(kmeans_stats_df)

# Summarize the stats and return in a data frame
kmeans_summary_stats_df <- summarize_clustering_stats(kmeans_stats_df)

# Preview the summary results
head(kmeans_summary_stats_df)

purity plots

# Plot individual cluster purity stats
kmeans_purity_plots <- plot_cluster_purity(kmeans_stats_df)

kmeans_purity_plots

silhouette width plots

# Plot individual cluster silhouette width stats
kmeans_silhouette_plots <- plot_cluster_silhouette_width(kmeans_stats_df)

kmeans_silhouette_plots

graph-based, walktrap

# Check the walktrap cluster validity stats for each of the clusters and return
# stats in a data frame
walktrap_stats_df <- create_metadata_stats_df(sample_290_normalized, c(5:25), 5, "walktrap")

Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"

  
# Preview the all stats results
head(walktrap_stats_df)

# Summarize the stats and return in a data frame
walktrap_summary_stats_df <- summarize_clustering_stats(walktrap_stats_df)

# Preview the summary results
head(walktrap_summary_stats_df)

purity plots

# Plot individual cluster purity stats
walktrap_purity_plots <- plot_cluster_purity(walktrap_stats_df)

walktrap_purity_plots

silhouette width plots

# Plot individual cluster silhouette width stats
walktrap_silhouette_plots <- plot_cluster_silhouette_width(walktrap_stats_df)

walktrap_silhouette_plots

graph-based, louvain

# Check the louvain cluster validity stats for each of the clusters and return
# stats in a data frame
louvain_stats_df <- create_metadata_stats_df(sample_290_normalized, c(5:25), 5, "louvain")

Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"
Joining, by = "cell_barcode"

# Preview the results
head(louvain_stats_df)

# Summarize the stats and return in a data frame
louvain_summary_stats_df <- summarize_clustering_stats(louvain_stats_df)

# Preview the summary results
head(louvain_summary_stats_df)

purity plots

# Plot individual cluster purity stats
louvain_purity_plots <- plot_cluster_purity(louvain_stats_df)

louvain_purity_plots

silhouette width plots

# Plot individual cluster silhouette width stats
louvain_silhouette_plots <- plot_cluster_silhouette_width(louvain_stats_df)

louvain_silhouette_plots

Check cluster stability

k-means

# Check and plot cluster stability
kmeans_cluster_names %>%
  purrr::walk(~ plot_cluster_stability(sample_290_normalized, .x))

graph-based, walktrap

walktrap_cluster_names %>%
  purrr::walk(~ plot_cluster_stability(sample_290_normalized, .x))

graph-based, louvain

louvain_cluster_names %>%
  purrr::walk(~ plot_cluster_stability(sample_290_normalized, .x))

Session info

sessionInfo()

R version 4.1.2 (2021-11-01)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.3 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

locale:
 [1] LC_CTYPE=C.UTF-8       LC_NUMERIC=C           LC_TIME=C.UTF-8        LC_COLLATE=C.UTF-8     LC_MONETARY=C.UTF-8   
 [6] LC_MESSAGES=C.UTF-8    LC_PAPER=C.UTF-8       LC_NAME=C              LC_ADDRESS=C           LC_TELEPHONE=C        
[11] LC_MEASUREMENT=C.UTF-8 LC_IDENTIFICATION=C   

attached base packages:
[1] stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] pheatmap_1.0.12             ggpubr_0.4.0                bluster_1.4.0               readr_2.1.1                
 [5] scater_1.22.0               ggplot2_3.3.5               scuttle_1.4.0               SingleCellExperiment_1.16.0
 [9] SummarizedExperiment_1.24.0 Biobase_2.54.0              GenomicRanges_1.46.1        GenomeInfoDb_1.30.0        
[13] IRanges_2.28.0              S4Vectors_0.32.3            BiocGenerics_0.40.0         MatrixGenerics_1.6.0       
[17] matrixStats_0.61.0          magrittr_2.0.1             

loaded via a namespace (and not attached):
 [1] bitops_1.0-7              RColorBrewer_1.1-2        bslib_0.3.1               tools_4.1.2              
 [5] backports_1.4.0           utf8_1.2.2                R6_2.5.1                  irlba_2.3.3              
 [9] vipor_0.4.5               DBI_1.1.1                 colorspace_2.0-2          nnet_7.3-16              
[13] withr_2.4.3               tidyselect_1.1.1          gridExtra_2.3             compiler_4.1.2           
[17] cli_3.1.0                 BiocNeighbors_1.12.0      DelayedArray_0.20.0       sass_0.4.0               
[21] labeling_0.4.2            scales_1.1.1              stringr_1.4.0             digest_0.6.29            
[25] rmarkdown_2.11            XVector_0.34.0            pkgconfig_2.0.3           htmltools_0.5.2          
[29] sparseMatrixStats_1.6.0   fastmap_1.1.0             rlang_0.4.12              rstudioapi_0.13          
[33] DelayedMatrixStats_1.16.0 jquerylib_0.1.4           farver_2.1.0              generics_0.1.1           
[37] jsonlite_1.7.2            BiocParallel_1.28.2       dplyr_1.0.7               car_3.0-12               
[41] RCurl_1.98-1.5            BiocSingular_1.10.0       modeltools_0.2-23         GenomeInfoDbData_1.2.7   
[45] Matrix_1.3-4              Rcpp_1.0.7                ggbeeswarm_0.6.0          munsell_0.5.0            
[49] fansi_0.5.0               abind_1.4-5               viridis_0.6.2             lifecycle_1.0.1          
[53] stringi_1.7.6             yaml_2.2.1                carData_3.0-4             zlibbioc_1.40.0          
[57] flexmix_2.3-17            grid_4.1.2                parallel_4.1.2            ggrepel_0.9.1            
[61] crayon_1.4.2              lattice_0.20-45           cowplot_1.1.1             beachmat_2.10.0          
[65] splines_4.1.2             hms_1.1.1                 knitr_1.36                pillar_1.6.4             
[69] igraph_1.2.9              ggsignif_0.6.3            ScaledMatrix_1.2.0        glue_1.5.1               
[73] evaluate_0.14             renv_0.14.0               vctrs_0.3.8               tzdb_0.2.0               
[77] gtable_0.3.0              purrr_0.3.4               tidyr_1.1.4               assertthat_0.2.1         
[81] xfun_0.28                 rsvd_1.0.5                broom_0.7.10              miQC_1.2.0               
[85] rstatix_0.7.0             viridisLite_0.4.0         tibble_3.1.6              beeswarm_0.4.0           
[89] cluster_2.1.2             ellipsis_0.3.2